PCR Primers: Conserved PCR Primers for Wheat SNP Discovery

Table 1: Conserved PCR primer sets (to be verified by PCR)

EST resources Mapped contig Mapped singletons Mapped single 5' EST Mapped single 3' EST Total sequences 4186 1859 6426 5814 Sequences matched 2 or more exons 2240 373 2092 1020 Total primers picked 1958 265 1624 705 Chr1 254 41 211 95 Chr2 295 43 237 103 Chr3 285 41 261 113 Chr4 334 44 272 117 Chr5 319 41 238 119 Chr6 226 28 189 77 Chr7 245 27 214 81 Unknown 0 0 2 0

Table 2: The success rates during conserved PCR primer design

Step Mapped contig Mapped singletons Mapped single 5' EST EST EST Mapped single 3' EST EST selected 4186 1859 6426 5814 Sucessful alignment of exons 54% 20% 33% 18% Conserved PCR primers (to be verified by PCR) 87% 71% 78% 69%

Conserved PCR primer lists for download: The four primer lists are provided for downloads.  These primers are saved in the four MS excel format files. 1. contig_primer_list.xls 2. singleton_primer_list.xls 3. single_est_5_primer_list.xls 4. single_est_3_primer_list.xls The document of conserved primer design is also available for download.